Preprints:

Peer Reviewed Papers:

 

 

The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol 25, 53 (2024). https://doi.org/10.1186/s13059-023-03113-6

Background

The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.

 

 

 

 

 

Tse V, Chacaltana G, Gutierrez M, Forino NM, Jimenez AG, Tao H, Do PH, Oh C, Chary P, Quesada I, Hamrick A, Lee S, Stone MD, Sanford JR. An Intronic RNA Element Modulates Factor VIII Exon-16 Splicing. Nucleic Acids Res. 2024 Jan 11;52(1):300-315. doi: 10.1093/nar/gkad1034. PMID: 37962303; PMCID: PMC10783525.

Graphical Abstract:

 

Palanichamy JK, Tran TM, King JK, Katzman S, Ritter AJ, Sharma G, Tso C, Contreras JR, Fernando TR, Sanford JR, Rao DS. Distinct oncogenic phenotypes in hematopoietic specific deletions of Trp53. Sci Rep. 2023 May 9;13(1):7490. doi: 10.1038/s41598-023-33949-8. PMID: 37160922; PMCID: PMC10169790.

Neeb ZT, Ritter AJ, Chauhan LV, Katzman S, Lipkin WI, Mishra N, Sanford JR. A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression. Sci Rep. 2022 Dec 15;12(1):21694. doi: 10.1038/s41598-022-26135-9. PMID: 36522444; PMCID: PMC9753033.

Figure 4: Proposed svRNA-miRNA interactions upon SARS-CoV-2 infection. 

 

Chang T, Draper JM, Van den Bout A, Kephart E, Maul-Newby H, Vasquez Y, Woodbury J, Randi S, Pedersen M, Nave M, La S, Gallagher N, McCabe MM, Dhillon N, Bjork I, Luttrell M, Dang F, MacMillan JB, Green R, Miller E, Kilpatrick AM, Vaske O, Stone MD, Sanford JR. A method for campus-wide SARS-CoV-2 surveillance at a large public university. PLoS One. 2021 Dec 17;16(12):e0261230. doi: 10.1371/journal.pone.0261230. PMID: 34919584; PMCID: PMC8682906.

Figure 1: Overview of the UC Santa Cruz Colligan clinical diagnostic laboratory workflow.

 

Tran TM, Philipp J, Bassi JS, Nibber N, Draper JM, Lin TL, Palanichamy JK, Jaiswal AK, Silva O, Paing M, King J, Katzman S, Sanford JR, Rao DS. The RNA-binding protein IGF2BP3 is critical for MLL-AF4-mediated leukemogenesis. Leukemia. 2022 Jan;36(1):68-79. doi: 10.1038/s41375-021-01346-7. Epub 2021 Jul 29. PMID: 34321607; PMCID: PMC8727287.

Howard JM, Lin H, Wallace A, Kim G, Draper JM, Katzman S, Hauessler M, Toloue M, Liu Y and Sanford JR. hnRNP A1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome Res. 2018. May;28(5):689-698. doi: 10.1101/gr.229062.117. Epub 2018 Apr 12. PMID: 29650551; PMCID: PMC5932609.

Martinez-Nunez, Wallace A, Coyne D, Jansson L, Rush M, Ennajdaoui H, Katzman S, Bailey J, Deinhardt K, Sanchez-Elsner T, Sanford JR. Modulation of nonsense mediated decay by rapamycin. Nucleic Acids Research. 2017. 2017 Apr 7;45(6):3448-3459. doi: 10.1093/nar/gkw1109

Rice ES, Kohno S, John JS, Pham S, Howard J, Lareau LF, O’Connell BL, Hickey G, Armstrong J, Deran A, Fiddes I, Platt RN 2nd, Gresham C, McCarthy F, Kern C, Haan D, Phan T, Schmidt C, Sanford JR, Ray DA, Paten B, Guillette LJ Jr, Green RE. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling.  Genome research. 2017; 27(5):686-696.

Ennajdaoui H, Howard JM, Sterne-Weiler T, Jahanbani F, Coyne DJ, Uren PJ, et al. IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell reports. 2016. doi: 10.1016/j.celrep.2016.04.083.

Graphical Abstract:

Highlights:

• IGF2BP3 promotes an invasive phenotype in pancreatic ductal adenocarcinoma cells

• IGF2BP3 regulates a malignancy-associated gene expression program in PDAC cells

• IGF2BP3 binding sites in PDAC cell lines are enriched near microRNA target sites

• IGF2BP3 modulates mRNA target association with Ago2

 

 

 

Palanichamy, J.K., Tran, T.M., Howard, J.M., Contreras, J.R., Fernando, T.R., Sterne-Weiler, T., Katzman, S., Toloue, M., Yan, W., Basso, G., Pigazzi, M., Sanford, J.R. and Rao, D.S. (2016). RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. The Journal of Clinical Investigation 126, 1495-1511.

Martinez-Nunez, R.T., and Sanford, J.R. (2016). Studying Isoform-Specific mRNA Recruitment to Polyribosomes with Frac-seq. Methods Mol Biol 1358, 99-108.

Hansen, H.T., Rasmussen, S.H., Adolph, S.K., Plass, M., Krogh, A., Sanford, J., Nielsen, F.C., and Christiansen, J. (2015). Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation. Genome biology 16, 123.

Sterne-Weiler, T., and Sanford, J.R. (2014). Exon identity crisis: disease-causing mutations that disrupt the splicing code. Genome biology 15, 201.

Figure 1: Targets of single-nucleotide polymorphism-induced aberrant pre-mRNA splicing mutations.

 

Mort M, Sterne-Weiler T, Li B, Ball EV, Cooper DN, Radivojac P, Sanford JR, Mooney SD. MutPred Splice: machine learning-based prediction of exonic variants that disrupt splicing. Genome Biol. 2014 Jan 13;15(1):R19.

Roberts J, Ennajdaoui H, Werth, B, Sanford JR and Chen B. Splicing factor TRA2B is required for neural progenitor survival. Journal of Comparative Neurology. 2014 Feb 1;522(2):372-92.

Sterne-Weiler T, Martinez-Nunez RT, Howard JM, Cvitovik I, Katzman S, Tariq MA, Pourmand N, Sanford JR. Frac-seq reveals isoform-specific recruitment to polyribosomes. Genome Res. 2013; 23 (10):1615-23. PMID: 23783272

Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. 2012. Site identification in high-throughput RNA-protein interaction data. Bioinformatics 28(23): 3013-3020.

St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed’hom B, Abzhanov A et al. 2012. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 13(1): 415.

Wang X, Juan L, Lv J, Wang K, Sanford JR, Liu Y. 2011. Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1. BMC Genomics 12 Suppl 5: S8.

Teng M, Wang Y, Wang G, Jung J, Edenberg HJ, Sanford JR, Liu Y. 2011. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC Proc 5 Suppl 9: S40.

Sterne-Weiler, T., J. Howard, M. Mort, D.N. Cooper, and J.R. Sanford. 2011. Loss of exon identity is a common mechanism of human inherited disease. Genome Res. 21: 1563-1571.

Wang, X., K. Wang, M. Radovich, Y. Wang, G. Wang, W. Feng, J.R. Sanford, and Y. Liu, Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. BMC Genomics, 2009. 10 Suppl 1: p. S4.

Sanford, J.R.*, X. Wang, M. Mort, N. Vanduyn, D.N. Cooper, S.D. Mooney, H.J. Edenberg, and Y. Liu, Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res, 2009.
*Corresponding author

Henao-Mejia, J., Y. Liu, I.W. Park, J. Zhang, J. Sanford, and J.J. He, Suppression of HIV-1 Nef translation by Sam68 mutant-induced stress granules and nef mRNA sequestration. Mol Cell, 2009. 33(1): p. 87-96.

Butler, J.S., L.R. Palam, C.M. Tate, J.R. Sanford, R.C. Wek, and D.G. Skalnik, DNA Methyltransferase protein synthesis is reduced in CXXC finger protein 1-deficient embryonic stem cells. DNA Cell Biol, 2009. 28(5): p. 223-31.

Wang, X., G. Wang, C. Shen, L. Li, X. Wang, S.D. Mooney, H.J. Edenberg, J.R. Sanford, and Y. Liu, Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics, 2008. 9 Suppl 1: p. S17.

Sanford, J.R*., P. Coutinho, J.A. Hackett, X. Wang, W. Ranahan, and J.F. Caceres, Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF. PLoS ONE, 2008. 3(10): p. e3369.
*Co-corresponding author

Michlewski, G., J.R. Sanford, and J.F. Caceres, The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol Cell, 2008. 30(2): p. 179-89.

Liang, F., Y. Luo, Y. Dong, C.D. Walls, J. Liang, H.Y. Jiang, J.R. Sanford, R.C. Wek, and Z.Y. Zhang, Translational control of C-terminal Src kinase (Csk) expression by PRL3 phosphatase. J Biol Chem, 2008. 283(16): p. 10339-46.

Sanford, J.R., J.D. Ellis, D. Cazalla, and J.F. Caceres, Reversible phosphorylation differentially affects nuclear and cytoplasmic functions of splicing factor 2/alternative splicing factor. Proc Natl Acad Sci U S A, 2005. 102(42): p. 15042-7.

Cazalla, D., J.R. Sanford, and J.F. Caceres, A rapid and efficient protocol to purify biologically active recombinant proteins from mammalian cells. Protein Expr Purif, 2005. 42(1): p. 54-8.

Blaustein, M., F. Pelisch, T. Tanos, M.J. Munoz, D. Wengier, L. Quadrana, J.R. Sanford, J.P. Muschietti, A.R. Kornblihtt, J.F. Caceres, O.A. Coso, and A. Srebrow, Concerted regulation of nuclear and cytoplasmic activities of SR proteins by AKT. Nat Struct Mol Biol, 2005. 12(12): p. 1037-44.

Sanford, J.R., N.K. Gray, K. Beckmann, and J.F. Caceres, A novel role for shuttling SR proteins in mRNA translation. Genes Dev, 2004. 18(7): p. 755-68.

Niksic, M., J. Slight, J.R. Sanford, J.F. Caceres, and N.D. Hastie, The Wilms’ tumour protein (WT1) shuttles between nucleus and cytoplasm and is present in functional polysomes. Hum Mol Genet, 2004. 13(4): p. 463-71.

Sanford, J.R. and J.P. Bruzik, Regulation of SR protein localization during development. Proc Natl Acad Sci U S A, 2001. 98(18): p. 10184-9.

Capellari, S., P. Parchi, C.M. Russo, J. Sanford, M.S. Sy, P. Gambetti, and R.B. Petersen, Effect of the E200K mutation on prion protein metabolism. Comparative study of a cell model and human brain. AmJ Pathol, 2000. 157(2): p. 613-22.

Sanford, J.R. and J.P. Bruzik, Developmental regulation of SR protein phosphorylation and activity. Genes Dev, 1999. 13(12): p. 1513-8.

Sanford, J.R. and J.P. Bruzik, SR proteins are required for nematode trans-splicing in vitro. Rna, 1999. 5(7): p. 918-28.

Solicited Papers:

The 3′ end of the story: deciphering combinatorial interactions that control mRNA fate
JR Sanford, LOF Penalva. Genome biology 18 (1), 227

From mechanisms to therapy: RNA processing’s impact on human genetics
LO Penalva, JR Sanford. Human genetics 136 (9), 1013-1014

Martiniez-Nunez and Jeremy R. Sanford. Studying isoform-specific mRNA recruitment to polyribosomes with Frac-seq. Vol. 1358, Erik Dassi (Eds): Post-Transcriptional Gene Regulation, 978-1-4939-3066-1, 322984_2_En, (6) In Press

Howard JM and Sanford JR. The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley interdisciplinary reviews RNA. 2014. doi: 10.1002/wrna.1260.

Sterne-Weiler T and Sanford JR. Exon identity crisis: disease-causing mutations that disrupt the splicing code. Genome biology. 2014;15(1):201. doi: 10.1186/gb4150.

Sanford, J.R., J. Ellis, and J.F. Caceres, Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem Soc Trans, 2005. 33(Pt 3): p. 443-6.

Sanford, J.R. and J.F. Caceres, Pre-mRNA splicing: life at the centre of the central dogma. J Cell Sci, 2004. 117(Pt 26): p. 6261-3.

Sanford, J.R., D. Longman, and J.F. Caceres, Multiple roles of the SR protein family in splicing regulation. Prog Mol Subcell Biol, 2003. 31: p. 33-58.

PATENTS

US Patent 9,765,398
Inventors: Jeremy R Sanford, Timothy Sterne-Weiler, UC Regents

Exonic splicing enhancers (ESE) and silencers (ESS) in disease causation, methods for identification of splicing sensitive disease mutations, and functional RNA elements as targets for amelioration of aberrant pre-mRNA splicing.